remove submissions with no assertion criteria when selecting ClinVar calls

[rjcorb]

Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #167. This PR modifies select-ClinVar-submissions.R to filter out those submissions with no assertion criteria provided

What was your approach?

Added filtering step when loading submissions summary:

dplyr::filter(!ReviewStatus %in% c("no assertion provided", "no assertion criteria provided"))

What GitHub issue does your pull request address?

167

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Please run select-ClinVar-submissions.R as follows:

Rscript select-clinVar-submissions.R --variant_summary input/variant_summary.txt.gz --submission_summary input/submission_summary.txt.gz

Then test that autogvp runs successfully with updated ClinVar-selected-submissions.tsv:

bash run_autogvp.sh --workflow="custom" \
--vcf=input/test_VEP.vcf \
--clinvar=input/clinvar.vcf.gz \
--intervar=input/test_VEP.hg38_multianno.txt.intervar \
--multianno=input/test_VEP.vcf.hg38_multianno.txt \
--autopvs1=input/test_autopvs1.txt \
--outdir=../results \
--out="test_custom"

Is there anything that you want to discuss further?

I think it makes sense to remove these submissions when evaluating majority calls, most recent calls, or calls with associated phenotype, for cases in which variants have conflicting interpretations. But if you have other thoughts please let me know.

Documentation Checklist

• [X] The function has examples to showcase the usage